rs4803224

chr19-39262374-G-Cchr19-39262374-G-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.198 in 151,726 control chromosomes in the GnomAD database, including 3,508 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.20 (3508 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.252

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.296 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.198 AC: 30038 AN: 151608 Hom.: 3513 Cov.: 30

Gnomad AFR AF: 0.0881

Gnomad AMI AF: 0.314

Gnomad AMR AF: 0.303

Gnomad ASJ AF: 0.202

Gnomad EAS AF: 0.107

Gnomad SAS AF: 0.283

Gnomad FIN AF: 0.181

Gnomad MID AF: 0.299

Gnomad NFE AF: 0.242

Gnomad OTH AF: 0.237

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.198 AC: 30038 AN: 151726 Hom.: 3508 Cov.: 30 AF XY: 0.197 AC XY: 14576 AN XY: 74114

Gnomad4 AFR AF: 0.0879

Gnomad4 AMR AF: 0.303

Gnomad4 ASJ AF: 0.202

Gnomad4 EAS AF: 0.107

Gnomad4 SAS AF: 0.283

Gnomad4 FIN AF: 0.181

Gnomad4 NFE AF: 0.242

Gnomad4 OTH AF: 0.235

Alfa AF: 0.218 Hom.: 495

Bravo AF: 0.204

Asia WGS AF: 0.164 AC: 571 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	3.1
Dann	Benign	0.59

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs4803224; hg19: chr19-39753014;